| Structural Analysis of RNA Loop-Loop Kissing Interactions How ribonucleic acid (RNA) molecules fold into tertiary structures, how proteins recognize specific RNA structures, and how protein binding is involved in RNA functions are central questions to a number of biological processes. Our research aims to elucidate structural and mechanistic principles that underlie the formation of a particular RNA structural fold, the loop-loop kissing motif, using multi-dimensional heteronuclear nuclear magnetic resonance (NMR) and fluorescence spectroscopy as the primary tools. RNA kissing interactions involved in plasmid copy number regulation in bacteria and in the dimerization of retroviral genomic RNA are being investigated. |
 | Structural Analysis of Polypurine-tract Recognition
Reverse transcriptase-associated ribonuclease H (RNase H) precisely removes the tRNA and polypurine tract (PPT) primers of (-)-strand and (+)-strand DNA synthesis, respectively, to generate the 3’ and 5’ terminal sequences of double stranded viral DNA essential for subsequent integration. The fidelity of these processing events is critical to a number of subsequent steps in retroviral replication cycle. Previous studies have shown that the PPT-containing RNA/DNA hybrids are specifically selected by their cognate RT’s, suggesting unique structural features are recognized by RT to orient the RNase H domain for specific cleavage at the PPT/U3 junction. Our research aims to understand the basis for specific Ty3 and HIV-1 PPT recognition and processing. |
 | Structural Analysis of GPCR Mediated Signal Transduction G-protein coupled receptors (GPCR’s) represent a diverse group of seven transmembrane helix receptors that require ligand-dependent activation to initiate heterotrimeric G-protein mediated intracellular signaling cascades. Due to their physiological relevance and pharmacological tractability, GPCR’s are the focus of numerous drug discovery efforts. The overall goal of our research is to develop and apply high-resolution nuclear magnetic resonance (NMR) methods to probe the structural basis for the propagation of structural signals from R* to the G-protein, with a specific focus on elucidating structural changes in the alpha subunit that lead to guanine nucleotide exchange. |
 | RNA as a Target for Small Molecule Therapeutics
The development of specific inhibitors of protein-RNA and RNA-RNA complexes is of significant interest as these complexes provide new and potentially powerful targets to regulate or inhibit gene expression. For instance, the inhibition of proteins that are involved in mRNA processing, DNA replication, RNA transcription and protein translation could provide powerful new drug targets to combat retroviral infections or fight cancer. Our research aims to develop and characterize fluorescence and NMR assays that are suitable for high-throughput screening of small molecules that bind to RNA and/or disrupt RNA-protein interactions. |
 | NMR Methodology Development
Our lab is interested in the development of new and improved NMR methods for acquiring novel structural and dynamical information about macromolecules and macromolecular interactions. Our work has focused on efforts to developed methods for determining trans H-bond scalar couplings, for measuring residual dipolar couplings, for improving 31P correlation and for analysis of 19F-labeled oligonucleotides. |
